Austin Whittall

The ultimate guide to Patagonia's cryptids, mythical beasts and legendary creatures.
From lake monsters to giants, from dwarves to surviving prehistoric beasts: a Patagonian bestiary.
If you find any useful information, or just like my blog, a link back would be great!

Thursday, November 26, 2015

I I have already posted about this
The link between Negritos, Papuans and Amerindians!, but the paper by P. Skoglund et al., published online on July 21, 2015 [1], found a close relationship between the genetic makeup of some Amazonian Native Americans and
a group of
Oceanian or Austalasian people. Namely, the team found "genome-wide data to show that some Amazonian Native Americans descend partly from a Native American founding population
that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans.
This signature is not present to the same extent, or at all, in present-day Northern and Central Americans or in a ~12,600-year-old Clovis-associated genome,
suggesting a more diverse set of founding populations of the Americas than previously accepted.".

Being beind a paywall, since that first posts I have read other online sources who have accessed the paper found some interesting points to share in this post:

Skoglund et al., found that the Amazonian Amerindians like the Suruí, the Xavante and Karitiana share around 1 or 2%
of their genes with aboriginal Andamanese, Papuans and Australians.
Furthermore, the 12,600 year-old remains from Anzic, Montana, US, don't have any links to these Australasians suggesting that the Anzic child and
modern Amazonians have different origins.

Their explanation is the following:

A simple migration from Melanesia north to Bering and then south into America does not seem likely because there are no traces of Australasian genes along
the route.
It is improbable that they would have covered such a long route without dallying with the locals and spreading their genes.

Instead they suggest that an ancestral population which is now extinct (that is why their genes cannot be found in Asia), lived in eastern Asia and split into
two groups, one that moved south into South East Asia, PNG and Australia and another that marched north across eastern Asia and entered America.

They named these mysterious people as "Population Y" (Y from the Tupi word "Ypykuéra", which means "ancestor").

As I am not constrained by the rigidity of orthodox science, I can suggest that there is a Denisovan link involved in this process:

As Austronesians have a very high share of Denisovan genetic input, the hypothetical "Population Y" may well be the group that admixed with Denisovans,
and therefore Denisovan genes in America could have
this origin.

An alternative explanation however for the lack of "Population Y" traces in Asia could be that the Denisovans lived both in Asia and America, and admixed
with the
first wave of humans that went into America and also with the first wave through their Asian homeland: the ancestors of the modern Australasians. Later, they became extinct, but their genes lived on. Later still,
Asians with a different genetic make up entered America and swept the first people away. Nowadays only 2% of the old genome survives in the Amazonian forests.

We have evidence of humans in Southern Asia aroung 120 kya, a very archaic population of humans; and they probably moved into America and mixed with Denisovans there or in Asia. What is the mtDNA of these people? If the hypothetical Out of Africa move took place earlier, then they could be Haplogroup M. We will have to wait for more evidence.

I found some very interesting pointers in the blog, and I want to share them with you:

On the rapid peopling of America once modern humans reached it: "There is a school of thought that population growth should have been rapid once humans entered the virgin landscape of the Americas"... "But there may be a problem with the assumption of rapid growth. It assumes that people could rapidly change their strategies to spread into the very different ecologies of inland North and South America.
Maybe it wasn’t so easy for them to develop the technical and organizational innovations necessary to move into those continental ecosystems."

This is a very interesting point. A coastal population living off the resources of the Pacific Ocean's coast, would have to devise new hunting - gathering techniques to tackle the Amazonian rainforest or the Argentine Puna or Patagonia (hunting guanaco and rhea).

An early peopling of America: "The earliest cranial remains we have from both North and South America are surprisingly variable in comparison to later peoples of the Americas. Those skulls suggest the possibility that they represent populations that had already experienced a lot of diversifying evolution by genetic drift. An earlier initial spread of humans across South America might explain that appearance.".

This is an interesting point. It is very clear that America was peopled in waves and not in "one go" from an isolated population in Beringia!.

John Hawks continues: "Could there have been an earlier habitation, now only present in living Native American peoples as traces of a “ghost population” that we haven’t yet identified?
If so, that scenario might explain the evidence for “deep divergence in Native American populations” that Rasmussen et al. (2014) found to predate the 12,600-year-old Clovis-associated Anzick-1 burial."

More sites like Monte Verde will be discovered (funding is scarce in South America) and we will find that humans have been living in the New World for much more than 50 ky. And the recent finding that humans have been living in Southern China for around 120 ky make this even more likely.

Wednesday, November 18, 2015

The third and last post of the day deals with a novel mtDNA sub clade found in the mummified (due to the high dry altitude of the Andes) remains of a child sacrificed by the Inca people about 500 years ago. The child's mtDNA is similar to that found in some very old remains in Upward Sun River, Alaska.

The paper (see below [1]), reports that this new variety of C1b haplogroup and that it is very ancient: The authors believe it originated some 14,000 years ago along the Andes in South America. As it is rare nowadays they suggest that either (a) it is due to a bias in sampling -so it has not been detected in large frequencies, or (b) it has become extinct in many parts due to the mass deaths caused by the turmoil of European discovery and conquest during th 1500s. They write:

" the phylogenetic patterns of C1bi point to a geographic origin in the Andean side of the South American sub-continent approximately 14 kya. The haplotype found in the Inca child from the Cerro Aconcagua, interpreted in the light of present-day variation in South America and together with the different archaeological and anthropological findings, supports the existence of demographic movements along the Pacific coastline during the Inca period. The fact that C1bi is very uncommon in present-day populations from South America could be explained by insufficient sampling of modern populations (although the present-day haplotype databases of mitogenomes and partial mtDNA sequences are very large). Alternatively, this rarity could reflect important changes in the gene pool of South America since the period of the Inca civilization. Further research on modern and ancient South American populations" [1]

Regarding the age, those 14 kya are maybe even too recent, their confidence intervals are rather wide, from 5 to 23.6 kya. The child was sacrificed 500 years ago during an Inca rite on the highest mountain located outside of Asia, the Aconcagua.

They point out that " C1b most likely arose relatively early, either in Beringia or at a very initial stage of the Paleoindian southward migration [...] While some C1b sub-clades were exclusively observed in Mesoamerica or in South America, a few of them were found in both territories." The map published in the paper shows the distribution of C1b across America: it is strongly concentrated in Mexico, Peru and strangely, in Puerto Rico.

C1b distribution heat map. From [1]

The child has a new clade named C1bi (where "i" stands for "Inca") and is similar to the clade "C1b13. The TMRCA of this sub-clade is 11.8 (8.6–15.1) kya; it is virtually absent from North-Central America and its geographic location is mainly centered in Chile", which fits in the same geograpic area of C1bi.

The clade is very rare: "By querying large databases of control region haplotypes (>150,000), we found only a few C1bi members in Peru and Bolivia (e.g. Aymaras), including one haplotype retrieved from ancient DNA of an individual belonging to the Wari Empire (Peruvian Andes)." [1]

I have already written about the loss of diversity in America not because of a Beringinan or Out of Asia bottleneck but due to the high death toll that virtually wiped out the Native Americans when they were contacted by the European navigators after 1492. Interestingly, my post cites a paper which points out that Hg C suffered a greater impact of lost diversity (with Hg D) than either haplogroups A or B.

In [1], the authors found one sample "...that belongs to haplogroup C1b13b sampled in a Spanish individual, although born in Talagante (Chile); therefore we labeled it here as originating in America" [1], in other words a person of European origin born in America carried a European variant of C1. They assumed perhaps that this individual had some Amerindian admixture, I believe that it is just a coincidence that this man has C1 and by chance his ancestors migrated to America.

The hot spot in Puerto Rico is very interesting and requires some explanation. The local Carib - Taino natives were wiped out early during the discovery period. So where did the C1b found there come from?

A paper published today (Kaifu Y, Kono RT, Sutikna T, Saptomo EW, Jatmiko, Due Awe R (2015) Unique Dental Morphology of Homo floresiensis and Its Evolvotionary Implications. PLoS ONE 10(11): e0141614. doi:10.1371/journal.pone.0141614) refutes a previous paper [2] that suggested that the Hobbit of the Indonesian Flores Island was a microcephalic human. Instead it suggests that the Hobbit was a primitive human species that underwent insular dwarfism.

To settle the issue of "new species" vs. "degenerate human" they took a peek at the Hobbit's teeth. And found that "H. floresiensis had primitive canine-premolar and advanced molar morphologies, a combination of dental traits unknown in any other hominin species. The primitive aspects are comparable to H. erectus from the Early Pleistocene, whereas some of the molar morphologies are more progressive even compared to those of modern humans."

Their paper disproves an even older origin (i.e. Australopithecines or H. habilis) but, and this is interesting their results suggest that " H. floresiensis derived from an earlier Asian Homo erectus population and experienced substantial body and brain size dwarfism in an isolated insular setting.".

They studied many variables and concluded that " the dental morphology of H. floresiensis is derived relative to H. habilis s. l. and is comparable to post-habilis grade Early Pleistocene Homo or H. erectus s. l. ...[giving] strong support to the hypothesis that H. floresiensis evolved from an early Javanese H. erectus population or a related form from the ancient Sundaland with substantial body and brain size dwarfism... "

The dwarfism is considerable, since an average Homo erectus is about 5.4 ft (1.65 m) tall and has a brain with 860 cm3 and the Hobbit is only 3.6 feet (1.1 m) tall and its brain is only 426 cm3.

But such insular dwarfism is not uncommon among mammals: elephants and hippopotamus that became midgets in Cyprus and mammoths that shrunk in Crete and on Flores itself, the dwarf stegodon (a relative of elephants).

Abstract
Denisovans, a sister group of Neandertals, have been described on the basis of a nuclear genome sequence from a finger phalanx (Denisova 3) found in Denisova Cave in the Altai Mountains. The only other Denisovan specimen described to date is a molar (Denisova 4) found at the same site. This tooth carries a mtDNA sequence similar to that of Denisova 3. Here we present nuclear DNA sequences from Denisova 4 and a morphological description, as well as mitochondrial and nuclear DNA sequence data, from another molar (Denisova 8) found in Denisova Cave in 2010. This new molar is similar to Denisova 4 in being very large and lacking traits typical of Neandertals and modern humans. Nuclear DNA sequences from the two molars form a clade with Denisova 3. The mtDNA of Denisova 8 is more diverged and has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over an extended period. The nuclear DNA sequence diversity among the three Denisovans is comparable to that among six Neandertals, but lower than that among present-day humans.

Take note of how large the Denisovan teeth are. From the paper

The paper notes that "Both Denisova 8 and Denisova 4 are very large compared with
Neandertal and early modern human molars, and Denisova 8 is even larger than Denisova 4. Only two Late Pleistocene third
molars are comparable in size: those of the inferred early Upper Paleolithic modern human Oase 2 in Romania and those of ObiRakhmat 1 in Uzbekistan"

The teeth though primitive looking also seem to differ from H. erectus teeth too. Which is quite interesting.

Denisova 8 is about 60,000 years older than Denisova 3 and Denisova 4 meaning that they are 110,000 years old. This is a long period of time in a same location.

The paper says the following about this long occupation: ", suggests Denisovans
were present in the area at least twice, and possibly over a long
time, perhaps interrupted by Neandertal occupation or occupations. Denisovans may therefore have been present in
southern Siberia over an extended period. Alternatively, they
may have been present in neighboring regions, from where they
may have periodically extended their range to the Altai.".

The paper ends with an open question: " Given that the
high-coverage genome from the Denisovan 3 phalanx carries a
component derived from an unknown hominin who diverged 1–4
million years ago from the lineage leading to Neandertals, Denisovans,
and present-day humans, it is possible that this component
differs among the three Denisovan individuals. In particular,
it may be that the older Denisovan population living in the cave
carried a larger or different such component. It is also possible that
the two diverged mtDNA lineages seen in Denisova 8 on the one
hand and Denisova 3 and Denisova 4 on the other were both introduced
into the Denisovans from this unknown hominin, as has
been suggested for the mtDNA of Denisova 3. However,
more nuclear DNA sequences from Denisovan specimens of ages
similar to Denisova 4 and Denisova 8 are needed to address this
question fully.".

Sunday, November 8, 2015

My recent post Africans reached America ca. 1310 C.E.? led to a comment by Ron Quiroriano, in which he wrote "Sickle cell anemia, is not an African only disease, its a natural defense against malaria, and is found through out tropical populations, it just reaches its peak distributions in Africans.", and this made me think about Malaria and the peopling of America. The outcome is today's post.

I had always believed that Malaria originated in Africa and that the only defense against it was the mutation that caused sickle cell anemia among Africans.
But I was mistaken. Actually there are several strains of Plasmodium that cause malaria in humans and, there are several mutations among humans to fend off the disease.

Malaria a brief overview

Malaria is caused by microorganisms (actually protozooans) of the genus Plasmodium they are transmitted by mosquito bites. The infected person will
suffer from fever, vomiting, fatigue and may even become severely ill and die.

There are different strains of Malaria, the worst is P. falciparum, which causes most deaths. The others: P. vivax, P. ovale, and P.
malariae are more benign and lead to a more mild illness. This, in my opinion indicates a more recent origin for P. falciparum, as it is too virulent.
The other strains have surely lived with us for a long time and evolved not to kill us (which is the best gambit for a parasite, why kill your host?).

The evolutionary pressure has selected positively some genetic traits among humans which give the carrier a better chance to reach maturity, mate and pass on those genes to their offspring.
These mutations are found among people living in areas where Malaria is endemic.

There are different mutations that give different resistence against the illness: sickle cell trait, thalassaemia traits, glucose-6-phosphate dehydrogenase deficiency, the lack of Duffy antigens on red blood cells and Ovalocytosis.

This wide range of mutations indicates that they have arisen in different groups of humans in different areas as a response to the pressure of this terrible disease.

map from (1) St George's University, 2007

So Sickle Cell is prevalent in Africa and some variants of Haemoglobin diseases (HbC, HbD and HbE) are found in Africa and Asia. The alpha and beta Thalassaemia
are found in a wide swath from Western Europe to Melanesia. All of them overlap the area where Malaria is predominant in the Old World.

But what about America? We will get there later. Now lets look at South East Asia.

Egg shaped red blood cells

Amato and Booth, (2) found that the hereditary Ovalocytosis is found among 5 to 20% of Melanesians in the coastal (malaria prone) areas of Papua New Guinea.
This is comparable to the frequency among Malaysian and Indonesians. The trait is also found in the Philippines.

It causes oval shaped blood cells, hence its name.

It is several hundred times more common than the sporadic type of oval shaped red blood cells (elliptocytosis) found in other populations (at a 0.02 - 0.05% frequency), a clear
indication that it is being selected for positively.

And as Rosanas-Urgell at al (2012) have proven by three independent studies (3): "strong associations between Southeast Asian ovalocytosis (SAO) and protection against P. vivax malaria by a mechanism that is independent of the Duffy antigen. P. vivax malaria may have contributed to shaping the unique host genetic adaptations to malaria in Asian and Oceanic populations."

The mention of Duffy antigen is because it was believed that this trait common in Africa indicated that P. vivax resistence evolved there, in the cradle of mankind when our distant human ancestors encountered P. Vivax, but it seems that this was not an Out Of Africa case. Actually it is quite the opposite.

And this is what Oleksyk, Smith and O'Brien (4) have asserted: "Plasmodium vivax is closely related to Asian primate malaria vectors, and Mu et al. (2005) have speculated that the pathogen may have emerged from Macaca to humans 53,000–265,000 years ago, and entered Africa afterwards."

But, as we will see below, the date may actually be much older. Anyway, 54 - 265 kya in South East Asia is very old, and takes us beyond the accepted date of an Out Of Africa event (ca. 60-100 kya). This means that P. vivax infected Homo erectus, which had been living in Asia for at least 1.5 million years.

From monkeys to Homo erectus

The ancient origin for Malaria infection among Hominids mentioned above is in line with Neafsey et al. (5) who compared P. Falciparum with P. vivax noticed some interesting differences between them:

"Other departures in the global population history of these two species are indicated by the topology and branch lengths of their respective phylograms...
The relatively large degree of divergence between the IQ07 Peruvian isolate and the Brazil I and Salvador I strains of P. vivax suggests a distinct history in the
New World relative to P. falciparum, which exhibits low diversity in the New World and is thought to have been introduced within the last 500 years via the African
slave trade." (5).

In other words, P. vivax has had more time to diversify and evolve in America than the more recently introduced P. Falciparum. And this is what they say (Bold is mine):

"The high New World diversity of P. vivax, combined with the closer phylogenetic affinity of the three New World P. vivax
isolates with the east Asian (North Korean) rather than the African (Mauritania I) or south Asian (India VII) strains, could suggest the precolonial
arrival of P. vivax in the New World accompanying human dispersal from Asia by sea or, less likely, by the Bering land bridge during the last glacial maximum." (5).

Or, may I add, perhaps an even older arrival (they are constrained by orthodoxy and a late peopling of America, I am not). Incidentally, they calculate for P. vivax,
"we can estimate the TMRCA as 768,000 years" (5), much older than the appearance of the first H. sapiens, and in line with H. erectus living in Asia.

This same theory, that Macaca passed it on to Hominids in South East Asia is also supported by other scholars like Escalante et al., who point out that the range of both species "overlapped,
especially, during the late Pliocene and middle Pleistocene (0.7–2.5 Myr), making possible the exchange of parasites in any direction" (6).
This period, once again, predates the appearance of Homo sapiens.

They are cautious however and state that "this investigation points to P. vivax being derived from ancestral macaque parasites when hominoids colonized Southeast Asia." (6) and
calculate a TMRCA "between 45,680 and 81,607 years ago, and possibly as old as "132,445" years, and they write "this time frame includes the accepted estimates for the introduction of H. sapiens in Southeast Asia; however, other hominoids were present such as H. erectus" (6).

Jongwutiwes et al., (2005) (7) take it up and give an even older age: "We estimated the age of the most recent common ancestor (MRCA) of the
mitochondrial genomes of both P. vivax and P. falciparum at around 200,000–300,000 years ago. This is close to previous estimates
of the time of the human mitochondrial MRCA and the origin of modern Homo sapiens, consistent with the hypothesis that both of these
Plasmodium species were parasites of the hominid lineage before the origin of modern Homo sapiens and that their population expansion
coincided with the population expansion of their host." (6).

They re-estimate Escalante's data and obtain "the age of the MRCA were 206,000–314,000 years (A.L. Hughes, unpublished), in good agreement with the present study" (7).

Which they conclude "P. vivax became a parasite of hominids – presumably in Asia – long before the origin of modern Homo sapiens. By about 1 Mya,
Homo erectus is known to have inhabited both Africa and a wide geographic area of southern Asia (Anton 2003).
We hypothesize that P. vivax transferred from a monkey host to H. erectus in Southeast Asia sometime before 1 Mya and subsequently
spread across southern Asia into Africa through the H. erectus population. This model assumes that P. vivax reached Africa by dispersal
through a H. erectus population that was distributed nearly continuously across Africa and southern Asia." (7)

So we have an ancient origin for P.vivax in South Asia, and evidence that it infected H. erectus over 300,000 years ago. Now lets look at its current endemicity:

Plasmodiium Vivax global Endemicity map, 2010.(8)

It is evident that the areas where P. vivax are endemic are Papua New Guinea, South East Asia and India. Which was the homeland of H. erectus.
In Africa it is present but at low rates, and... surprisingly, it is very prevalent in America, in eastern Central America and in the Amazon basin. So How did it reach America?

P. vivax in America

A very interesting thesis by Petr Triska (9) looks into the Plasmodiums in America and concludes that "P. falciparum has
been endemic to Americas for more than 600 years." (9), it is a Precolombine infection with later events of colonization due to African slave trade.

Regarding P. vivax Triska writes: "that Plasmodium vivax was
present in Americas prior European colonization and prior documented contacts with Polynesia.
Colonization of Americas from Africa is not supported in our network. Ancestral haplotype of
Americas is not shared with Africa. Furthermore, majority of slaves dragged to Americas were
embarked in West Africa, however, West Africans are highly resistant to P.vivax and P. vivax is not prevalent there." (9)

He finds no support for a recent (last 600 years) migration from Polynesia. Neither did he find any "suggestion that present day American population of malaria
parasites emerged from African strains" (9). He finds "Population ages were in magnitude of tens of thousands years", a clear indication that
it is very old.

The Homo erectus link

Another protection from Malaria is given by O blood group. Apparently (Cserti-Gazdewich et al. 2011) Heterozygotes 00 grants
resistance against malaria while A0, B0 and AB probably have no resistance. Since Amerindians are almost exclusively O group (
80-100%), we can suppose it is due to positive selection against Malaria. Curiously, another hot spot for high O blood group is in Northern Australia and Melanesia.

Global O Blood Group distribution. (10)

So, we have evidence that P. vivax infected Homo erectus in South East Asia. That it reached America long ago, that it did not come via Polynesia or Africa. So it reached
the New World from Asia. That it is prevalent in the deep Amazon, meaning it got there long ago, when it was first inhabited.
That South East Asians and Melanesians have a mutation (oval shaped red blood cells) that protects them against P. vivax Malaria.

And, incredibly, this strange "ovalocytosis" mutation found in South East Asia, has been detected in Mexico, in two patients with no ties with S.E. Asia! pure Native American Mexicans:

Lets quote Ramos-Kuri et al. (11): "We describe the finding of two Mexican patients with a specific 27-bp deletion in the solute carrier family 4 gene (SLC4A1Δ27) (also known as the band 3 gene found on chromosome 17q21–q22), characteristic of Southeast Asian ovalocytosis (SAO). The patients were asymptomatic, and the initial diagnosis was made by microscopic observation of the presence of typical stomatocytic ovalocytes. The gene deletion was confirmed by PCR and DNA sequencing. Both patients were heterozygous for the deletion. One patient is from Tabasco state, in southeastern Mexico, a malaria-endemic zone. The other patient is from Mexico City, which is not a malaria-endemic area. Their families have no non-Mexican ancestors and their previous generations were born in Mexico. Both patients carry the HLA-B*3501 subtype, characteristic of Amerindians and Asian populations. Familial and HLA data led us to conclude that these two patients are the first report of SLC4A1Δ27 in Amerindians. The nucleotide analysis showing a perfect match sequence between Southeast Asian and Mexican patients suggests, but does not prove, that the Mexican gene is not a de novo mutation. Instead, this gene might be the result of migration of individuals with Asian ancestry into the Mexican gene pool. We are looking for other families with the mutation to detect, by HLA analysis, the ancient ethnic origin of these patients." (11).

Does this imply that the mutation was carried to America by a common ancestor of both South East Asians and Amerindians? Or is it the outcome of an even older carrier that admixed with Native Americans in America?
I am suggesting that Homo erectus reached America with this mutation and passed it on to Amerindians later, when modern H. sapiens reached the New World.

Sunday, November 1, 2015

I have read several blogs posting about the Olmec "heads" as an example of an early presence of Africans in America (this is a typical example). I usually consider those theories a bit outlandish and shrug them off with little effort. But today I found something a bit more scientific; A paper by Dr. Clyde Winter who looks into the HLA variants to pinpoint an African expedition to Mesoamerica around 1310 AD.

Apparently Abubakari II, ruler of Mali in Africa sent an expedition to America in 1310 and that is the source of admixture in Mesoamerica (not the later slave trade that brought millions of unfortunate Africans to work and die in the New World;
read more about this African king.

For a good explanation on African - Native American admixture, see this website. The first Africans to reach America did so in what is now Santo Domingo Island in 1502. Some escaped, met the local natives and that led to the first admixture.

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